Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016314.1 Corchorus olitorius cultivar O-4 contig16347, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 1773
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37


Found at i:367 original size:24 final size:25

Alignment explanation


    Indices: 321--371  Score: 68
    Period size: 24  Copynumber: 2.1  Consensus size: 25

        311 ATTGGAGTAT

                           *         
        321 TTATTTATCTTGTTGCTTAATTTTA
          1 TTATTTATCTTGTTGATTAATTTTA

                          *   *      
        346 TTATTT-TCTTGTTTATTTATTTTA
          1 TTATTTATCTTGTTGATTAATTTTA

              
        370 TT
          1 TT

        372 TTTCACATAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  24   17  0.74
  25    6  0.26

ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71


Consensus pattern (25 bp):   
TTATTTATCTTGTTGATTAATTTTA

Found at i:1292 original size:28 final size:28

Alignment explanation


    Indices: 1224--1293  Score: 72
    Period size: 28  Copynumber: 2.5  Consensus size: 28

       1214 TATGGGCATA

                   *                    
       1224 AAATTACCGTTTTACCCTAAGAATGAAT
          1 AAATTACAGTTTTACCCTAAGAATGAAT

                               *      ** 
       1252 AAATTACCA-TTTTACCCTTAGAA-GGTT
          1 AAATTA-CAGTTTTACCCTAAGAATGAAT

                           
       1279 AAATTTACAGTTTTA
          1 AAA-TTACAGTTTTA

       1294 ACTTTGTACT


Statistics
Matches: 35,  Mismatches: 4, Indels: 6
        0.78            0.09        0.13

Matches are distributed among these distances:
  27    7  0.20
  28   27  0.77
  29    1  0.03

ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37


Consensus pattern (28 bp):   
AAATTACAGTTTTACCCTAAGAATGAAT
Done.